Sunday, February 27, 2011

Super-SILAC Technology for Quantitative Proteomics in Neoplasms

A group of investigators under Dr. Matthias Mann at Max Planck Institute of Biochemistry in Martinsried, Germany is working on an interesting quantitative proteomics technology that might offer a new way to analyze cell proteins in a range of disorders, such as cancer and autoimmune diseases. Called super-SILAC (stable-isotope labeling by amino acids in cell culture), the method generates thousands of isotopically labeled peptides in unique amounts to serve as "internal standards for mass spectrometry-based analysis."

Thursday, February 24, 2011

Research scientists develop powerful new methodology for stabilizing proteins

A team of scientists at The Scripps Research Institute has discovered a new way to stabilize proteins - the workhorse biological macromolecules found in all organisms. Proteins serve as the functional basis of many types of biologic drugs used to treat everything from arthritis, anemia, and diabetes to cancer.
As described in the February 4, 2011 edition of the journal Science, when the team attached a specific oligomeric array of sugars called a "glycan" to proteins having a defined structure, the proteins were up to 200 times more stable in the test tube. In the body, this stability may translate into longer half-lives for therapies, possibly lowering the overall cost of treatment for certain protein-based drugs and requiring patients to have fewer injections during a course of treatment.
The work may have major implications for the drug industry because there are a large number of protein-based drugs on the market, more in clinical trials, and many more under development worldwide. Nearly all of these protein-based drugs have glycans attached to them and are therefore called "glycoproteins". Glycoprotein-based drugs can be quite expensive to produce and usually need to be administered intravenously.
One of the challenges in producing these drugs has been increasing their stability, which generally extends their half-life in the bloodstream - issues that the new discovery appears to address directly.
"We've now provided engineering guidelines for glycoprotein stability," said Scripps Research Professor Jeffery W. Kelly, who is chair of the Department of Molecular and Experimental Medicine, Lita Annenberg Hazen Professor of Chemistry, and member of The Skaggs Institute for Chemical Biology at Scripps Research. Kelly led the study with Scripps Research Associate Professor Evan Powers and Staff Scientist Sarah R. Hanson, in collaboration with Research Associates Elizabeth K. Culyba, Joshua Price, and colleagues.

Thursday, February 17, 2011

Canadian Human Proteome Project Workshop

Canadian Human Proteome Project Workshop Part 2, MaRS District Discovery, TorontoFebruary 22, 2011
MaRS District Discovery
Toronto, Ontario

The Canadian National Proteomics Network is promoting a Canadian Human Proteomics Project (CHPP), which will leverage Canada’s existing strengths in proteomics, health research and technology. A position paper is currently being developed based on the outcomes of the first CHPP Workshop held on January 16-17, 2011 in conjunction with the Annual Proteomics Conference in Cell Biology in Barbados. The CHPP Working Group will present the first draft of this position paper and invite feedback and further development of the project from the research community, clinicians and industry partners. As members of the CNPN and CNPN Board of Directors, the goal of the organizers of the Workshop is to present a final version of the position paper to Canadian and provincial funding agencies in the Spring of 2011 with the intent of stimulating interest for a nationwide funding competition to support a CHPP.

We invite you to participate in the development of a CHPP during our full-day Workshop on February 22. The Workshop will consist of presentations from leaders around the world participating in the
 Human Proteome Project, discussion of the goals and potential projects for CHPP, and key strategies for engaging national funding agencies and industry partners. 

Sunday, February 13, 2011

Highly Sensitive & Specific Chromatin Immunoprecipitation (ChIP) Assay Kit from Porvair Filtration Group

orvair Filtration Group has developed a new technology that has particular relevance to the rapidly expanding Epigenetics market and will be unveiling it at the Epigenetics World Congress in Boston in April 2011. Using a new approach, based on a rigid porous polymer matrix rather than the traditional sepharose or magnetic beads, Porvair has developed a novel Chromatin ImmunoPrecipitation (ChIP) assay kit called Chromatrap™.

Friday, February 11, 2011

ESS++: a C++ objected-oriented algorithm for Bayesian stochastic search model exploration

Summary: ESS++ is a C++ implementation of a fully Bayesian variable selection approach for single and multiple response linear regression. ESS++ works well both when the number of observations is larger than the number of predictors and in the ‘large p, small n’ case. In the current version, ESS++ can handle several hundred observations, thousands of predictors and a few responses simultaneously. The core engine of ESS++ for the selection of relevant predictors is based on Evolutionary Monte Carlo. Our implementation is open source, allowing community-based alterations and improvements.
Availability: C++ source code and documentation including compilation instructions are available under GNU licence at

DNAnexus Launches First Complete Cloud-Based Solution for Genomic Variation Identification

DNAnexus, Inc. announces the availability of a comprehensive set of new informatics tools that enable life science researchers to efficiently analyze and manage large-scale genomic variation datasets in a cloud-based workflow. DNAnexus will discuss results from a study using this solution at the 12th annual Advances in Genome Biology and Technology (AGBT) meeting in Marco Island, Florida. 
read more

Saturday, February 5, 2011

That's How Breast Cancer Cells Roll

When cancer metastasizes, cells break off from the primary tumor, travel through the lymphatic or circulatory system, and then invade other tissue. Now researchers have found a protein that allows breast cancer cells to roll along blood vessel walls—a key step in the metastatic process (Anal. Chem., DOI: 10.1021/ac102901e).
Cancer cells take a page from white blood cells' playbook when it comes to tissue invasion. When responding to an injury, leukocytes cling loosely to the cells lining a blood vessel wall and then, propelled by the shear force of the rushing fluid, roll along it like Velcro-covered soccer balls. They continue until they can attach tightly enough to worm their way between the wall's cells and into the surrounding tissue. To perform these cellular acrobatics, two proteins must interact: selectins, which protrude from vessel wall cells, and their ligands, which leukocytes and circulating tumor cells express on their surfaces.

Meetings/workshops on bioinformatics and computational biology in China

1.go to top of page[ID=365924]ICBBE — 5th Intl Conference on Bioinformatics and Biomedical Engineering
10 May 2011 → 11 May 2011; Wuhan, China
2.go to top of page[ID=385350]5th International Conference On Bioinformatics And Biomedical Engineering
10 May 2011 → 12 May 2011; Wuhan, China
3.go to top of page[ID=372265]iCCBE 2011 — The 5th International Conference on Bioinformatics and Biomedical Engineering
13 May 2011 → 15 May 2011; Wuhan, China
4.go to top of page[ID=398091]CBB2011 — 2011 International Conference on Computational Biology and Bioinformatics
28 Oct 2011 → 30 Oct 2011; Shanghai, China
abstract: The 2011 International Conference on Computational Biology and Bioinformatics (CBB2011) will take place in Shanghai China, 28-30 October, 2011. The conference CBB2011 is held under the World Congress on Engineering and Technology 2011(CET2011). The CET 2011 is composed of several conferences on the frontier topics in the engineering and technological subjects.

Thursday, February 3, 2011

Uniquant: an alternative to MaxQuant

UNiquant, a Program for Quantitative Proteomics Analysis Using Stable Isotope Labeling


Abstract Image
Stable isotope labeling (SIL) methods coupled with nanoscale liquid chromatography and high resolution tandem mass spectrometry are increasingly useful for elucidation of the proteome-wide differences between multiple biological samples. Development of more effective programs for the sensitive identification of peptide pairs and accurate measurement of the relative peptide/protein abundance are essential for quantitative proteomic analysis. We developed and evaluated the performance of a new program, termed UNiquant, for analyzing quantitative proteomics data using stable isotope labeling. UNiquant was compared with two other programs, MaxQuant and Mascot Distiller, using SILAC-labeled complex proteome mixtures having either known or unknown heavy/light ratios. For the SILAC-labeled Jeko-1 cell proteome digests with known heavy/light ratios (H/L = 1:1, 1:5, and 1:10), UNiquant quantified a similar number of peptide pairs as MaxQuant for the H/L = 1:1 and 1:5 mixtures. In addition, UNiquant quantified significantly more peptides than MaxQuant and Mascot Distiller in the H/L = 1:10 mixtures. UNiquant accurately measured relative peptide/protein abundance without the need for postmeasurement normalization of peptide ratios, which is required by the other programs.

Keywords (keywords): 

Quantitative proteomics; Stable isotope labeling; LC-MS/MS; Software Development

mzServer: Web-based Programmatic Access for Mass Spectrometry Data Analysis


Continued progress towards systematic generation of large-scale and comprehensive proteomics data in the context of biomedical research will create project-level data sets of unprecedented size and ultimately overwhelm current practices for results validation that are based on distribution of native or surrogate mass spectrometry files. Moreover, the majority of proteomics studies leverage discovery-mode MS/MS analyses, rendering associated data-reduction efforts incomplete at best, and essentially ensuring future demand for re-analysis of data as new biological and technical information become available. Based on these observations, we propose to move beyond the sharing of interpreted spectra, or even the distribution of data at the individual file or project level, to a system much like that used in high-energy physics and astronomy, whereby raw data are made programmatically accessible at the site of acquisition. Towards this end we have developed a web-based server (mzServer), which exposes our common API (mzAPI) through very intuitive (RESTful) URLs and provides remote data access and analysis capabilities to the research community. Our prototype mzServer provides a model for lab-based and community-wide data access and analysis. A live instance of the mzServer can be accessed directly at: The data associated with this manuscript may be downloaded from the Tranche network using the following hash: 6g+QpUvlpxc6PM/M9t/49h0PMLwA7dTCgpwyUqfciXEyZpLun7QzPz8E+LDDJfZzBf1lGKe7t1OkXbmomzTEy70Av/kAAAAAAAAYtg== In addition, the data are available here: